AMMU: A survey of transformer-based biomedical pretrained language models.

Transformer-based pretrained language models (PLMs) have started a new era in modern natural language processing (NLP). These models combine the power of transformers, transfer learning, and self-supervised learning (SSL). Following the success of these models in the general domain, the biomedical research community has developed various in-domain PLMs starting from BioBERT to the latest BioELECTRA and BioALBERT models. We strongly believe there is a need for a survey paper that can provide a comprehensive survey of various transformer-based biomedical pretrained language models (BPLMs). In this survey, we start with a brief overview of foundational concepts like self-supervised learning, embedding layer and transformer encoder layers. We discuss core concepts of transformer-based PLMs like pretraining methods, pretraining tasks, fine-tuning methods, and various embedding types specific to biomedical domain. We introduce a taxonomy for transformer-based BPLMs and then discuss all the models. We discuss various challenges and present possible solutions. We conclude by highlighting some of the open issues which will drive the research community to further improve transformer-based BPLMs. The list of all the publicly available transformer-based BPLMs along with their links is provided at https://mr-nlp.github.io/posts/2021/05/transformer-based-biomedical-pretrained-language-models-list/.

The New Version of the ANDDigest Tool with Improved AI-Based Short Names Recognition.

The body of scientific literature continues to grow annually. Over 1.5 million abstracts of biomedical publications were added to the PubMed database in 2021. Therefore, developing cognitive systems that provide a specialized search for information in scientific publications based on subject area ontology and modern artificial intelligence methods is urgently needed. We previously developed a web-based information retrieval system, ANDDigest, designed to search and analyze information in the PubMed database using a customized domain ontology. This paper presents an improved ANDDigest version that uses fine-tuned PubMedBERT classifiers to enhance the quality of short name recognition for molecular-genetics entities in PubMed abstracts on eight biological object types: cell components, diseases, side effects, genes, proteins, pathways, drugs, and metabolites. This approach increased average short name recognition accuracy by 13%.

A Multi-Label Text Classifier at Publication Level Based on "PubMedBERT + TextRNN" for Cancer Literature.

There is a rapid growth in the volume of data in the cancer field and fine-grained classification is in high demand especially for interdisciplinary and collaborative research. There is thus a need to establish a multi-label classifier with higher resolution to reduce the burden of screening articles for clinical relevance. This research trains a multi-label classifier with scalability for classifying literature on cancer research directly at the publication level. Firstly, a corpus was divided into a training set and a testing set at a ratio of 7:3. Secondly, we compared the performance of classifiers developed by "PubMedBERT + TextRNN" and "BioBERT + TextRNN" with ICRP CT. Finally, the classifier was obtained based on the optimal combination "PubMedBERT + TextRNN", with P= 0.952014, R=0.936696, F1=0.931664. The quantitative comparisons demonstrate that the resulting classifier is fit for high-resolution classification of cancer literature at the publication level to support accurate retrieving and academic statistics.

An audio-semantic multimodal model for automatic obstructive sleep Apnea-Hypopnea Syndrome classification via multi-feature analysis of snoring sounds.

Introduction: Obstructive Sleep Apnea-Hypopnea Syndrome (OSAHS) is a common sleep-related breathing disorder that significantly impacts the daily lives of patients. Currently, the diagnosis of OSAHS relies on various physiological signal monitoring devices, requiring a comprehensive Polysomnography (PSG). However, this invasive diagnostic method faces challenges such as data fluctuation and high costs. To address these challenges, we propose a novel data-driven Audio-Semantic Multi-Modal model for OSAHS severity classification (i.e., ASMM-OSA) based on patient snoring sound characteristics. Methods: In light of the correlation between the acoustic attributes of a patient's snoring patterns and their episodes of breathing disorders, we utilize the patient's sleep audio recordings as an initial screening modality. We analyze the audio features of snoring sounds during the night for subjects suspected of having OSAHS. Audio features were augmented via PubMedBERT to enrich their diversity and detail and subsequently classified for OSAHS severity using XGBoost based on the number of sleep apnea events. Results: Experimental results using the OSAHS dataset from a collaborative university hospital demonstrate that our ASMM-OSA audio-semantic multimodal model achieves a diagnostic level in automatically identifying sleep apnea events and classifying the four-class severity (normal, mild, moderate, and severe) of OSAHS. Discussion: Our proposed model promises new perspectives for non-invasive OSAHS diagnosis, potentially reducing costs and enhancing patient quality of life.

BioBBC: a multi-feature model that enhances the detection of biomedical entities.

The rapid increase in biomedical publications necessitates efficient systems to automatically handle Biomedical Named Entity Recognition (BioNER) tasks in unstructured text. However, accurately detecting biomedical entities is quite challenging due to the complexity of their names and the frequent use of abbreviations. In this paper, we propose BioBBC, a deep learning (DL) model that utilizes multi-feature embeddings and is constructed based on the BERT-BiLSTM-CRF to address the BioNER task. BioBBC consists of three main layers; an embedding layer, a Long Short-Term Memory (Bi-LSTM) layer, and a Conditional Random Fields (CRF) layer. BioBBC takes sentences from the biomedical domain as input and identifies the biomedical entities mentioned within the text. The embedding layer generates enriched contextual representation vectors of the input by learning the text through four types of embeddings: part-of-speech tags (POS tags) embedding, char-level embedding, BERT embedding, and data-specific embedding. The BiLSTM layer produces additional syntactic and semantic feature representations. Finally, the CRF layer identifies the best possible tag sequence for the input sentence. Our model is well-constructed and well-optimized for detecting different types of biomedical entities. Based on experimental results, our model outperformed state-of-the-art (SOTA) models with significant improvements based on six benchmark BioNER datasets.